While conceptualizing the novel, Stepheson studied philosophy tomes and later applied his research to the story, which is a science fiction setting. In an interview, he stated that he has no interest in philosophical readings, joking that he "read them so you don't have to." His research also included speaking with members of the Long Now Foundation, a non-profit cultural institution in San Francisco.

Anathem received mostly positive reviews. Some praised Stepheson for his original concepts and abstract worldview, while others remarked that the prose was too dense, the story insubstantial. Paul Botin of The Wall Street Journal called Anathem "a page turner and philosophical argument," while Michael Dirda of The Washington Post found Anathem to be "grandiose, overwrought, and pretty damn dull." The novel peaked at #1 on the New York Times Bestseller List for hardcover fiction.

Anathem received the Locus Award for Best Science Fiction in 2009, as well as the Hugo, Arthur C. Clarke, and John W. Campbell Memorial Awards.